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Fluorine in PDB 5o8z: Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.

Protein crystallography data

The structure of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator., PDB code: 5o8z was solved by P.Casino, A.Marina, L.Miguel-Romero, J.Huesa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.392, 54.266, 54.986, 62.60, 81.61, 79.66
R / Rfree (%) 21.3 / 26.5

Other elements in 5o8z:

The structure of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. (pdb code 5o8z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator., PDB code: 5o8z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 1 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:28.8
occ:1.00
 F1 A:BEF301 0.0 28.8 1.0
BE A:BEF301 1.5 28.3 1.0
MG A:MG302 2.0 30.6 1.0
F2 A:BEF301 2.4 28.4 1.0
F3 A:BEF301 2.6 29.2 1.0
OD1 A:ASP56 2.7 25.9 1.0
OD2 A:ASP56 2.9 27.5 1.0
O A:HOH428 2.9 29.1 1.0
O A:HOH418 3.0 26.0 1.0
O A:SER58 3.0 31.3 1.0
CG A:ASP56 3.1 26.6 1.0
CB A:SER58 3.5 34.6 1.0
N A:SER58 3.6 33.3 1.0
CE A:MET88 3.7 38.9 1.0
C A:SER58 3.8 32.6 1.0
CA A:SER58 3.8 33.6 1.0
O A:HOH422 3.9 44.4 1.0
NZ A:LYS109 4.1 28.7 1.0
OG A:SER58 4.1 37.2 1.0
OD1 A:ASP11 4.1 29.2 1.0
CB A:ASP56 4.6 27.2 1.0
CG A:MET88 4.6 34.6 1.0
N A:LEU57 4.7 30.8 1.0
SD A:MET88 4.8 39.7 1.0
C A:LEU57 4.8 32.8 1.0
OG1 A:THR87 5.0 31.7 1.0
OD2 A:ASP10 5.0 28.4 1.0

Fluorine binding site 2 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 2 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:28.4
occ:1.00
 F2 A:BEF301 0.0 28.4 1.0
BE A:BEF301 1.5 28.3 1.0
F1 A:BEF301 2.4 28.8 1.0
OD1 A:ASP56 2.5 25.9 1.0
F3 A:BEF301 2.5 29.2 1.0
OG1 A:THR87 2.8 31.7 1.0
O A:HOH422 2.8 44.4 1.0
N A:SER58 3.0 33.3 1.0
N A:LEU57 3.2 30.8 1.0
CB A:LEU57 3.4 34.5 1.0
CG A:ASP56 3.5 26.6 1.0
CA A:LEU57 3.6 32.8 1.0
CB A:THR87 3.6 30.7 1.0
C A:LEU57 3.7 32.8 1.0
OG A:SER58 3.8 37.2 1.0
CA A:THR87 3.9 29.7 1.0
CB A:SER58 3.9 34.6 1.0
CA A:SER58 4.0 33.6 1.0
OD2 A:ASP56 4.0 27.5 1.0
N A:MET88 4.1 30.1 1.0
MG A:MG302 4.2 30.6 1.0
C A:ASP56 4.3 29.0 1.0
O A:SER58 4.3 31.3 1.0
O A:LEU86 4.5 29.2 1.0
CA A:ASP56 4.6 27.4 1.0
CB A:ASP56 4.6 27.2 1.0
C A:THR87 4.6 29.6 1.0
C A:SER58 4.6 32.6 1.0
N A:ASN89 4.7 33.1 1.0
CG A:MET88 4.7 34.6 1.0
CG A:LEU57 4.7 37.9 1.0
NZ A:LYS109 4.9 28.7 1.0
O A:LEU57 4.9 33.8 1.0

Fluorine binding site 3 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 3 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:29.2
occ:1.00
 F3 A:BEF301 0.0 29.2 1.0
BE A:BEF301 1.5 28.3 1.0
F2 A:BEF301 2.5 28.4 1.0
F1 A:BEF301 2.6 28.8 1.0
OD1 A:ASP56 2.7 25.9 1.0
NZ A:LYS109 2.8 28.7 1.0
N A:MET88 2.9 30.1 1.0
CE A:LYS109 3.2 28.8 1.0
CE A:MET88 3.3 38.9 1.0
CD A:LYS109 3.4 28.7 1.0
CG A:MET88 3.4 34.6 1.0
CA A:THR87 3.4 29.7 1.0
C A:THR87 3.6 29.6 1.0
OG1 A:THR87 3.6 31.7 1.0
CB A:MET88 3.7 33.7 1.0
CG A:ASP56 3.7 26.6 1.0
CA A:MET88 3.8 31.9 1.0
O A:HOH418 3.9 26.0 1.0
OD2 A:ASP56 4.1 27.5 1.0
CB A:THR87 4.1 30.7 1.0
SD A:MET88 4.2 39.7 1.0
O A:LEU86 4.2 29.2 1.0
MG A:MG302 4.2 30.6 1.0
O A:HOH422 4.2 44.4 1.0
CG A:LYS109 4.4 28.8 1.0
N A:THR87 4.5 29.3 1.0
OD2 A:ASP10 4.6 28.4 1.0
N A:ASN89 4.7 33.1 1.0
C A:MET88 4.7 33.0 1.0
C A:LEU86 4.8 29.9 1.0
O A:THR87 4.8 28.6 1.0
O A:HOH416 4.9 32.1 1.0
N A:LEU57 4.9 30.8 1.0
CB A:ASP56 5.0 27.2 1.0

Fluorine binding site 4 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 4 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:27.4
occ:1.00
 F1 B:BEF301 0.0 27.4 1.0
BE B:BEF301 1.5 27.6 1.0
MG B:MG302 2.0 32.3 1.0
F2 B:BEF301 2.4 28.1 1.0
F3 B:BEF301 2.6 26.8 1.0
OD1 B:ASP56 2.8 25.6 1.0
OD2 B:ASP56 2.8 27.4 1.0
O B:SER58 3.0 30.5 1.0
O B:HOH420 3.1 31.3 1.0
CG B:ASP56 3.1 26.7 1.0
O B:HOH432 3.1 26.4 1.0
CB B:SER58 3.3 33.9 1.0
N B:SER58 3.4 31.2 1.0
CA B:SER58 3.6 32.5 1.0
CE B:MET88 3.7 37.0 1.0
C B:SER58 3.7 31.5 1.0
OG B:SER58 3.9 36.7 1.0
OD1 B:ASP11 4.1 26.8 1.0
NZ B:LYS109 4.1 24.6 1.0
N B:LEU57 4.5 28.5 1.0
CB B:ASP56 4.6 27.0 1.0
CG B:MET88 4.6 34.2 1.0
C B:LEU57 4.6 31.2 1.0
OD1 B:ASN89 4.7 48.1 1.0
SD B:MET88 4.8 37.2 1.0
ND2 B:ASN89 5.0 45.6 1.0

Fluorine binding site 5 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 5 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:28.1
occ:1.00
 F2 B:BEF301 0.0 28.1 1.0
BE B:BEF301 1.5 27.6 1.0
F1 B:BEF301 2.4 27.4 1.0
F3 B:BEF301 2.4 26.8 1.0
OD1 B:ASP56 2.6 25.6 1.0
OG1 B:THR87 2.7 24.3 1.0
N B:SER58 3.0 31.2 1.0
N B:LEU57 3.2 28.5 1.0
CB B:LEU57 3.5 30.8 1.0
ND2 B:ASN89 3.5 45.6 1.0
CG B:ASP56 3.5 26.7 1.0
CA B:LEU57 3.6 30.2 1.0
CB B:THR87 3.6 24.9 1.0
CG B:ASN89 3.8 45.1 1.0
C B:LEU57 3.8 31.2 1.0
OD1 B:ASN89 3.8 48.1 1.0
CA B:THR87 3.9 24.8 1.0
OG B:SER58 3.9 36.7 1.0
OD2 B:ASP56 4.0 27.4 1.0
CB B:SER58 4.0 33.9 1.0
CA B:SER58 4.0 32.5 1.0
N B:MET88 4.0 28.4 1.0
MG B:MG302 4.2 32.3 1.0
C B:ASP56 4.3 28.0 1.0
CG B:LEU57 4.5 31.6 1.0
O B:SER58 4.5 30.5 1.0
C B:THR87 4.5 26.4 1.0
CA B:ASP56 4.6 26.9 1.0
CG B:MET88 4.6 34.2 1.0
N B:ASN89 4.6 35.5 1.0
CB B:ASP56 4.6 27.0 1.0
C B:SER58 4.7 31.5 1.0
O B:LEU86 4.7 22.9 1.0
CB B:ASN89 4.7 41.9 1.0
NZ B:LYS109 4.9 24.6 1.0
CD1 B:LEU57 5.0 32.2 1.0
O B:LEU57 5.0 31.3 1.0

Fluorine binding site 6 out of 6 in 5o8z

Go back to Fluorine Binding Sites List in 5o8z
Fluorine binding site 6 out of 6 in the Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Conformational Dynamism For Dna Interaction in Salmonella Typhimurium Rcsb Response Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:26.8
occ:1.00
 F3 B:BEF301 0.0 26.8 1.0
BE B:BEF301 1.5 27.6 1.0
F2 B:BEF301 2.4 28.1 1.0
F1 B:BEF301 2.6 27.4 1.0
OD1 B:ASP56 2.7 25.6 1.0
NZ B:LYS109 2.8 24.6 1.0
N B:MET88 2.9 28.4 1.0
CE B:LYS109 3.2 24.4 1.0
CE B:MET88 3.2 37.0 1.0
CG B:MET88 3.4 34.2 1.0
CD B:LYS109 3.5 25.1 1.0
CA B:THR87 3.5 24.8 1.0
C B:THR87 3.7 26.4 1.0
CB B:MET88 3.7 32.8 1.0
CG B:ASP56 3.7 26.7 1.0
OG1 B:THR87 3.8 24.3 1.0
CA B:MET88 3.9 31.9 1.0
O B:HOH432 3.9 26.4 1.0
MG B:MG302 4.0 32.3 1.0
OD2 B:ASP56 4.1 27.4 1.0
SD B:MET88 4.2 37.2 1.0
CB B:THR87 4.2 24.9 1.0
O B:LEU86 4.3 22.9 1.0
CG B:LYS109 4.6 25.2 1.0
OD1 B:ASN89 4.6 48.1 1.0
N B:THR87 4.6 24.4 1.0
O B:HOH409 4.6 36.7 1.0
N B:ASN89 4.7 35.5 1.0
OD2 B:ASP10 4.7 26.0 1.0
C B:MET88 4.7 33.4 1.0
O B:THR87 4.8 25.9 1.0
C B:LEU86 4.9 24.0 1.0
N B:LEU57 5.0 28.5 1.0
CB B:ASP56 5.0 27.0 1.0

Reference:

P.Casino, L.Miguel-Romero, J.Huesa, P.Garcia, F.Garcia-Del Portillo, A.Marina. Conformational Dynamism For Dna Interaction in the Salmonella Rcsb Response Regulator. Nucleic Acids Res. V. 46 456 2018.
ISSN: ESSN 1362-4962
PubMed: 29186528
DOI: 10.1093/NAR/GKX1164
Page generated: Thu Aug 1 12:16:27 2024

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